Tue Nov 22 14:12:37 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:12:42 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5826895 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 0.5826895 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.77779 90.22482 90.52503 assigned negative charge : -288.4263 centred at (gu) : 89.78848 90.30146 90.63922 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4458 nv = 96 ne = 84 npr = 40156 no. pairs analyzed = 40156 no. exposed pairs = 2421 no. arc points = 17343 no. surface atoms = 817 nbur = 1147 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 173 mr = 2406 m= 0 mr = 12 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1797 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5541 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2060986E-09 -1.2211382E-09 midg,1,midg; midg,igrid,midg 1.8225021E-09 -5.0127297E-10 1,midg,midg; igrid,midg,midg 9.4804287E-10 5.3999999E-10 gauss-seidel spectral radius is 0.9847126 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:12:45 rms-change max change #iterations 8.2049772E-02 14.24402 at 10iterations 6.4817951E-03 1.098679 at 20iterations 5.1199459E-04 9.3488693E-02 at 30iterations 3.9026872E-05 6.3095093E-03 at 40iterations 3.1618199E-06 5.5885315E-04 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 3.1618199E-06 5.5885315E-04 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 14:12:56 3.025u 0.140s 0:14.40 21.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:13:01 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.748069 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 1.748069 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.33344 90.67441 91.57530 assigned negative charge : -288.4263 centred at (gu) : 89.36578 90.90459 91.91788 start vw surface at 0.1200000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 48585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17343 grid for indexing accessible points = 1.400000 m= 16487 mr = 33102 m= 1895 mr = 12345 m= 33 mr = 1121 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2800 time to turn everything in is 0.3400000 number of dielectric boundary points 20427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14189 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5826895 object centre at (A) : 5.269001 0.7995005 17.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0145585E-03 -5.4964279E-03 midg,1,midg; midg,igrid,midg 3.0610559E-03 -1.2978071E-03 1,midg,midg; igrid,midg,midg 3.4976266E-02 2.3044312E-02 gauss-seidel spectral radius is 0.9983021 estimated iterations to convergence 193 setup time was (sec) 0.6000000 now iterating at: 14:13:08 rms-change max change #iterations 3.055497 160.6567 at 10iterations 1.306483 56.61572 at 20iterations 0.5617098 22.83269 at 30iterations 0.2403744 9.767890 at 40iterations 0.1029308 4.125583 at 50iterations 4.4392996E-02 1.858185 at 60iterations 1.8976999E-02 0.8391628 at 70iterations 8.1379823E-03 0.3192024 at 80iterations 3.4899588E-03 0.1412654 at 90iterations 1.4900927E-03 6.0791016E-02 at 100iterations 6.3949078E-04 2.4417877E-02 at 110iterations 2.7509473E-04 1.1327744E-02 at 120iterations finished qdiffx linear iterations at : 14:13:27 total time elapsed so far: 6.560000 # loops : 120 mean,max change (kT/e) : 2.7509473E-04 1.1327744E-02 energy calculations done at 6.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 14:13:35 6.734u 0.158s 0:34.43 19.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:13:37 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.622103 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 2.622103 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.00012 91.01151 92.36293 assigned negative charge : -288.4263 centred at (gu) : 89.04862 91.35693 92.87692 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 112527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17343 grid for indexing accessible points = 1.400000 m= 55412 mr = 80339 m= 17559 mr = 45681 m= 3033 mr = 14276 m= 172 mr = 2238 m= 4 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 9310 time to turn everything in is 0.8200000 number of dielectric boundary points 46078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14647 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.748069 object centre at (A) : 5.269001 0.7995005 17.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0632393E-02 -5.6007579E-02 midg,1,midg; midg,igrid,midg 2.6872301E-02 -1.6516343E-02 1,midg,midg; igrid,midg,midg 0.4107172 0.2600999 gauss-seidel spectral radius is 0.9991425 estimated iterations to convergence 270 setup time was (sec) 1.130000 now iterating at: 14:13:44 rms-change max change #iterations 7.448812 246.1682 at 10iterations 4.116088 121.2719 at 20iterations 2.268628 53.14642 at 30iterations 1.246543 30.15788 at 40iterations 0.6877576 16.01672 at 50iterations 0.3765624 8.849680 at 60iterations 0.2060604 4.831731 at 70iterations 0.1131808 2.677485 at 80iterations 6.2175613E-02 1.367561 at 90iterations 3.4132596E-02 0.8119717 at 100iterations 1.8678641E-02 0.4103127 at 110iterations 1.0238389E-02 0.2377651 at 120iterations 5.6219497E-03 0.1403542 at 130iterations 3.0867397E-03 6.8381786E-02 at 140iterations 1.6961725E-03 3.7498474E-02 at 150iterations 9.3248207E-04 2.0202637E-02 at 160iterations 5.1321957E-04 1.2216568E-02 at 170iterations 2.8103357E-04 6.0310364E-03 at 180iterations finished qdiffx linear iterations at : 14:14:17 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 2.8103357E-04 6.0310364E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 14:14:23 12.458u 0.226s 0:46.32 27.3% 0+0k 0+0io 0pf+0w